Diarrheal diseases are responsible for more than two billion cases every year and constitute one of the main global health challenges. The disease is particularly common in developing countries, where it disproportionally affects young children who, on average, get diarrhea three times a year. Diarrhea results from an infection in the intestinal tract, which can be caused by a variety of bacteria, viruses and eukaryotic parasites. In most studies, less than half of the diarrhea cases can be attributed to a known pathogen, partially due to the limitations of current detection approaches that i) only test a handful of known pathogens and/or ii) fail to differentiate among closely related species with different pathogenicity. Here, we propose to apply a novel genomic assay developed in our laboratory to screen 3,600 stool samples collected by the GEMS study in four countries from infants with diarrhea and matched controls. Our assay enables detection and characterization of all eukaryotic parasites present in a sample, regardless of whether they have been previously characterized (and may therefore reveal novel pathogens). It also provides sufficient resolution to differentiate closely-related organisms that are typically lumped together. Combined with a detailed characterization of the gut bacterial communities, our studies will provide a comprehensive perspective on the contribution of eukaryotic parasites to intestinal dysbiosis and diarrhea, and may highlight novel therapeutic avenues to fight this disease.